I'm adding JSON-LD markup to some software products I have created in the store I'm using to distribute them, following the structured data guidelines from Google. But I also have separate help pages on another site for these software products. Should I add the structured data there as well?
Why do you want to add it twice? Product structured data on product page is absolutely enough.
Beside of this help page is not a product page, so it would be only possible to use another kind of main type, like Webpage.
Sure you will be able to tie both page through something like
mainContenOfPage orabout` or similar. But i don't see very much sense in it.